After you get some equipment, you reach the Deku Tree, who asks you to break the curse upon him.
Get the Map
There is a Deku Baba ahead and to the left. This one will bite at you, so to avoid getting hurt, raise your shield when you target it. Cut it twice to kill it.
There is a ladder near where the Deku Baba was. Climb up, then follow the path until you reach a chest. Open the chest for the dungeon map.
Get the Fairy Slingshot
Don't climb the wall vines yet. Instead, continue on the circular path until you reach a door. Navi explains how to go through doors. Go through.
There is a Deku Scrub in here. Target it and raise your shield, and the deku nut will bounce off of your shield and hit the Deku Scrub. Go up to it and talk to it to learn how to roll when landing from a high fall (hold the control stick forward) to prevent getting hurt. Go through the door that opens.
Jump across the stone in the air to reach the ledge across from where you started. If it falls before you go across, just climb the vines. Open the chest to get the Fairy Slingshot.
Get the Compass
If you want a recovery heart, climb up the vines near the treasure chest that you just opened. Open the small chest there to get a recovery heart. Then climb back down to where you opened the treasure chest.
Turn around to face the door that you came in. Target the green spot that appears, and fire your slingshot to knock down the ladder. Jump down, and you can cut the bushes here to get more Deku Seeds for your Slingshot. Then climb the ladder to get out of this room. In the next room, just go through the door to get out.
From the door, you can do some target practice. Try to kill the spider-like Skulltulas that are on the vines above where you got the map earlier. There are three Skulltulas on the vines. Try to get them all. Then go to those vines, kill any Skulltulas you missed, and climb up to the top level. After you reach a certain height, you will have to climb sideways (to the right) until you're over the platform. Let go and go around the circle until you see a door. Go through.
In here, step on the switch to raise three platforms temporarily. Don't go to the treasure chest on the left yet. Instead, jump across to the far wall where there is a bigger chest. Open it to get the compass.
Get a Gold Skulltula
If you have no Deku Sticks, kill the Deku Baba to the right of the compass chest and collect the stick. Then jump down to ground level. To the right, there is a Skulltula (look for its shadow on the ground). Get close, but not too close, until you lure it down, and then wait for it to turn around and expose its belly. Attack its belly with your sword. You'll need to do this twice to kill it. Never get too close to it or it will do a spin attack.
Next, kill the Deku Baba, then climb up the nearby vines to return to the area where you entered the room, and once again step on the switch to raise the platforms. This time, jump over to the alcove to the left. You will hear a scraping sound, which means that there is a gold Skulltula nearby. Gold skulltulas don't attack, although if you touch them, you will get hurt. They die after two hits from the Kokiri Sword. Once you kill it, it leaves behind a gold token. Take it. There are 100 gold skulltulas scattered around Hyrule. The more gold tokens you collect, the more rewards you will receive later. There is a chest in the alcove where the gold skulltula was, containing a recovery heart.
Get a Second Gold Skulltula
To leave the room, climb back up to where you entered and equip a deku stick. Walk to the burning torch so that the end of the stick touches the flames. Then walk over to the unlit torch and use the burning end of the deku stick to light the unlit torch. This opens the door. Put away your Deku Stick by pressing A. Otherwise the fire will burn it and you will lose it. Go through the door.
There are three normal (non-gold) Skulltulas at this upper level, each guarding a ledge. Find one and kill it. Then, run off of the edge of the ledge and as soon as you jump, let go of the control stick. This should situate you right above the spiderwebs all the way on the first floor so that you land on them and break through them. If not, you will get hurt and have to climb all the way back up and jump off a ledge again.
When you get through the webs and land in the water, climb up onto the platform with the Deku Baba on it. Kill it, then aim your slingshot at the vines above, where there is a gold Skulltula. Kill it, then climb up the vines to get the token.
Get a Third Gold Skulltula
Drop back down into the water. There is a shallow area behind you. Walk on it toward the bars that are at one side of the room. Use the slingshot on the gold Skulltula, then to get the token that it leaves behind, you have to climb up onto the ledge to the right of it. Go up against the wall next to the bars, then make a running jump toward the token and you should be able to reach it.
Reach the Dungeon Boss
Get back on the ledge you just jumped from and step on the switch. This will light the torch on this platform, revealing a small chest containing a recovery heart. Light a deku stick and jump down to the shallow part of the water. Jump across to the area with the spiderwebs blocking the door. Burn the web down and go through the door.
Use your shield to kill this Deku Scrub and learn "2 3 1". To open the door, use the slingshot on the eye above it. Go through.
In this room, you have to lower the water level to get under the spiked bar. To do that, walk left from the entrance and walk down the slope that leads into the water. Swim forward and you'll see a switch below you in the water. Before diving to it, turn and face the slope you just came down. Then, move so that your shadow is over the switch, then dive to hit the switch. As soon as you can, go up the slope and face the moving platform. The water stays down for a while, so don't be hasty. When the platform is near, jump onto it, take it across, and when you're near, jump to the other side.
Kill the Skulltula in front of you, then walk over to the left side of the big block. Push the block along the path in the ground until it stops, then climb onto it, and climb up to the ledge with the door. Go through.
Kill the center Deku Baba, and if you need Deku Sticks, kill the other two Babas in here. They regenerate after you kill them, so you can get as many deku sticks as you need here. Light the two unlit torches, and go through the door.
Kill the Skulltula ahead of you. It has its belly turned to you, so you can slash it as soon as it comes down to your level. It does turn around, so be careful not to hit its skull-marked back. Stay around the edge of this room. If you go to the center, monsters will fall on you.
Heading left around the edge, kill the Deku Baba. Use a Deku Stick on the torch, then go around to the first wall of spiderwebs. Burn them down, although you won't be able to go any farther beyond them until you come back to this dungeon later with an item. Then put away your Deku Stick and walk back to the torch. Get out another deku stick and light it, then quickly go around the room to the second wall of spiderwebs. Burn it down and put away the Deku Stick, then crawl through the hole that you revealed.
In this room, be careful not to fall off of the ledge or you will have to backtrack to return to this area. Push the block over the ledge to create a shortcut (which makes it so you won't have to backtrack if you fall off), then go to the torch across the way and light a Deku Stick. Go back the way you came, climbing up the block you pushed, and do a rolling attack (press A while running) over the webs on the floor, and the deku stick will touch the web and burn it. Press A before the web burns if you want to prevent the Deku Stick from burning away. You'll fall to the bottom floor.
Dive to get any recovery hearts you need, then go up the slope. This is where you need to remember "2 3 1". Start by targeting the second (middle) Deku Scrub and raise your shield to deflect the deku nut and turn it blue. Then, target the third Scrub (far right) and raise your shield. Finally, target the first (far left) Scrub and do the same. Walk up to that final Scrub to learn the strategy for beating Gohma. When that's done, replenish any hearts you need, and go through the door.
Before you go through the opening to the larger area, you can look up by pressing the View button in the touchscreen in the 3DS version or by pressing C-up in the N64 version and see Gohma silently glowing on the ceiling. Once you go through the opening, you hear Gohma moving.
To start the battle, you have to press View in the touchscreen in the 3DS version or C-up in the N64 version and look at Gohma's orange eye. Then Gohma will land in front of you. Target her right away, and when her eye turns red, hit it with the slingshot to stun her.
While she is stunned, hit her eye with the sword as many times as you can.
Afterward, stay locked onto Gohma. She will crawl away and will climb to the ceiling. When she reaches the ceiling, make sure that Gohma is facing you. Shoot Gohma's eye when it turns red. Then run up to Gohma and hit her eye repeatedly with the sword again.
She will drop monsters from the ceiling if you don't knock her off of the ceiling quickly enough when her eye turns red.
After you defeat Gohma, get the heart container that is left behind. Then walk into the glowing blue circle to be transported outside of the tree.